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Life Sciences Commons™

Open Access. Powered by Scholars. Published by Universities.®

2016

Selected Works

Ray Enke Ph.D.

Articles 1 - 17 of 17

Full-Text Articles in Life Sciences

Heat Map Analysis Of Rna-Seq Data Using Rstudio, Ray A. Enke, Ashton Holub Nov 2016

Heat Map Analysis Of Rna-Seq Data Using Rstudio, Ray A. Enke, Ashton Holub

Ray Enke Ph.D.

This in class exercise focuses on using the CummeRbund package in RStudio to create heat maps for analyzing differential gene expression output generated by Cuffdiff in DNA Subway Green Line

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Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie*, Annamarie Meinsen*, Emily R. Grunwald*, Stephen Turner, Raymond A. Enke Nov 2016

Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie*, Annamarie Meinsen*, Emily R. Grunwald*, Stephen Turner, Raymond A. Enke

Ray Enke Ph.D.

RNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis. Existing retinal transcriptome projects have been critical to the vision research community for studying aspects of murine and human retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal transcriptome. Here we used Illumina RNA sequencing …

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Intro To Rstudio, Ray A. Enke, Ashton Holub Nov 2016

Intro To Rstudio, Ray A. Enke, Ashton Holub

Ray Enke Ph.D.

This in class exercise is designed to teach novices about the basic features of R and RStudio using a non-biological data set called Gapminder. It is a modified version of a Data Carpentry Workshop that I use to teach programming to beginners.

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Connecting Common Genetic Polymorphisms To Protein Function: A Modular Project Sequence For Lecture Or Lab, Christopher E. Berndsen, Byron H. Young, Quinlin Mccormick*, Raymond A. Enke Oct 2016

Connecting Common Genetic Polymorphisms To Protein Function: A Modular Project Sequence For Lecture Or Lab, Christopher E. Berndsen, Byron H. Young, Quinlin Mccormick*, Raymond A. Enke

Ray Enke Ph.D.

Single nucleotide polymorphisms (SNPs) in DNA can result in phenotypes where the biochemical basis may not be clear due to the lack of protein structures. With the growing number of modeling and simulation software available on the internet, students can now participate in determining how small changes in genetic information impact cellular protein structure and function. We have developed a modular series of activities to engage lab or lecture students in examining the basis for common phenotypes. The activities range from basic phenotype test- ing/observation to DNA sequencing and simulation of protein structure and dynamics. We provide as an exam- …

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Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Ray A. Enke Oct 2016

Sequence Annotation & Designing Gene-Specific Qpcr Primers (Computational), Ray A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Obtaining and annotating genomic DNA and mRNA sequence information
  • Designing primers for quantitative PCR (qPCR) analysis of a cDNA library

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Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Ray A. Enke Oct 2016

Qpcr Primer Standard Curve Assay (Wet Lab) + Kegg Pathway Analysis (Computational), Ray A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • analyzing qPCR standard curve data to determine primer efficiency
  • analyzing differential gene expression experimental qPCR data
  • applying KEGG pathway analysis of selected candidates genes

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Research & Course-Based Applicatons Of The Ucsc Genome Browser, Ray A. Enke Jun 2016

Research & Course-Based Applicatons Of The Ucsc Genome Browser, Ray A. Enke

Ray Enke Ph.D.

No abstract provided.

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Approaches To Teaching Rna-Seq In Undergraduate Lecture & Lab Courses, Ray A. Enke May 2016

Approaches To Teaching Rna-Seq In Undergraduate Lecture & Lab Courses, Ray A. Enke

Ray Enke Ph.D.

No abstract provided.

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Qpcr Analysis Of Differential Gene Expression (Wet Lab), Raymond A. Enke May 2016

Qpcr Analysis Of Differential Gene Expression (Wet Lab), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Analyze qPCR data to determine normalized gene expression for candidate genes identified from an RNA-Seq data set
  • Set up additional or repeat experimental qPCR reactions
  • Create a draft poster outlining the methods & data collected during the 6-week RNA-Seq analysis lab module

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1st Strand Cdna Synthesis From Total Rna (Wet Lab), Raymond A. Enke May 2016

1st Strand Cdna Synthesis From Total Rna (Wet Lab), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
• Construct a cDNA library representative of total cellular messenger RNAs

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Pathway Analysis Of Differentially Expressed Genes (Computational), Raymond A. Enke May 2016

Pathway Analysis Of Differentially Expressed Genes (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Conduct gene ontology (GO) pathway analysis of statistically and biologically significant differentially expressed genes (DEGs)
  • Sort and organize lists of DEGs in MS Excel spreadsheets based on biological function

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Dissection & Rna Isolation From Embryonic Chicken Retina (Wet Lab), Raymond A. Enke May 2016

Dissection & Rna Isolation From Embryonic Chicken Retina (Wet Lab), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Dissect retina & cornea from developing chicken embryos
  • Extract total cellular RNA from tissues for downstream gene expression analysis

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Rna Gel & Spectrophotometer Analysis (Wet Lab), Raymond A. Enke May 2016

Rna Gel & Spectrophotometer Analysis (Wet Lab), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Determine quantity & purity of total RNA using a spectrophotometer
  • Determine the quality of total RNA using native agarose gel electrophoresis (no formaldehyde required)

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Analysis Of Rna-Seq Alignments Using Dna Subway Green Line (Computational), Raymond A. Enke May 2016

Analysis Of Rna-Seq Alignments Using Dna Subway Green Line (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Review basic steps of RNA-Seq bioinformatics analysis in DNA Subway Green Line
  • View and run basic analytics of RNA-Seq data set in DNA Subway Green Line

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Bitter Taste Receptor Genotype/Phenotype Lab: A Modular Project Sequence For Lecture Or Lab, Raymond A. Enke May 2016

Bitter Taste Receptor Genotype/Phenotype Lab: A Modular Project Sequence For Lecture Or Lab, Raymond A. Enke

Ray Enke Ph.D.


Single nucleotide polymorphisms (SNPs) in DNA can result in phenotypes where the biochemical basis may not be clear due to the lack of protein structures. With the growing number of modeling and simulation software available on the internet, students can now participate in determining how small changes in genetic information impact cellular protein structure and function. We have developed a modular series of activities to engage lab or lecture students in examining the basis for common phenotypes.  The activities range from basic phenotype testing/observation to DNA sequencing and simulation of protein structure and dynamics. We provide as an example study …

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Creating Custom Rna-Seq Data Tracks In The Ucsc Genome Browser (Computational), Raymond A. Enke May 2016

Creating Custom Rna-Seq Data Tracks In The Ucsc Genome Browser (Computational), Raymond A. Enke

Ray Enke Ph.D.

This class tested protocol will guide students through the steps for the following activities:
  • Create your own custom data tracks in the UCSC Genome Browser
  • Visualize RNA-Seq TopHat alignment data as custom tracks in the UCSC Genome Browser
  • Integrate RNA-Seq alignment data with other genome-wide data sets

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Integration Of Rna-Seq Data Analysis Into Undergraduate Lab Teaching Modules, Raymond A. Enke Jan 2016

Integration Of Rna-Seq Data Analysis Into Undergraduate Lab Teaching Modules, Raymond A. Enke

Ray Enke Ph.D.


Undergraduate students learn about Next Generation Sequencing (NGS) platforms in courses, but often have difficulty understanding the impact of these techniques without hands-on experience analyzing actual NGS datasets.  The NSF-supported Infrastructure & Training to Bring NGS Analysis Into Undergraduate Education project focuses on streamlining RNA-sequencing (RNA-seq) data analysis using a combination of bioinformatics and wet lab workflows tailored for implementation into diverse undergraduate laboratory classroom settings. These modular workflows can be applied to a variety of novel or publicly available RNA-seq datasets.
 
To create a course-based undergraduate research experience focusing on NGS that complements my research program, I …

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